I don't have any experience missing Jpn domestic flight, but I have no reasons to believe it's any more lenient there than in the US. In fact, I believe I've missed a flight probably 2-3 times within the last 5-10 years in the US (most likely they were United domestic flights) and each time I think I was allowed to board the next flight as a stand-bye for free.

In Jpn, I heard LCC's are very strict on this. I can't speak to JAL or ANA, but I feel like ANA's regular check-in counter staff at NRT are becoming a bit more hard-a** lately. But I'm sure people's experiences vary, and HND's domestic check-in agents could very well be better to deal with than NRT's.

Anyways, if it were me, I'd really pad my connection time (like 3.5+ hrs) but would take a chance.